[BiO BB] Can you explain theses results?

[Benoit VARVENNE]

Hi Daniel,

Have you thought about the limit of hits while running a Blast ?
I mean that the default limit is (I think) 500hits for a query so, if you
reach this limit, the Blast is stopped and the results returned.

I think this can explain that there is less time of execution when you reach
these 500hits.
While running a remote Blast, I think this limit can be changed but I don't
remember what's the option.

Hope this will help,
Cheers

Benoît

-- 
Benoit Varvenne,
Bioinformatics,
GenOway - Lyon (France)
 

Le 26/04/07 17:08, « Daniel Xavier de Sousa » <danielucg at yahoo.com.br> a
écrit :

> Hi for all
> 
> Please, you would see theses tests in serial machine, but important to
> cluster. 
> What do you think about it?
> 
> Please look theses tests using BLASTP:
> 
> Length Seq Query  -- HITs -- TIME
> 10000                   -- 3    -- 8min51sec
> 10000                   -- 500  -- 7min41sec
> ----------------------------------
> Length Seq Query  -- HITs -- TIME
> 9000                      --  2   --
> 7min11sec
> 9000                      --  500 -- 6min49sec
> ----------------------------------
> Length Seq Query  -- HITs -- TIME
> 3000                      --  3   -- 2min54sec
> 3000                     --  500 -- 2min52sec
> 
> Theses
> times are very strange. You can see which the sequence of 10000 bases
> and 3 hits get more time than another sequence of 10000 bases but with
> 500 hits. So, I can conclude: BLASTP is not sensitive to similarity,
> difference of BLASTN.
> 
> But the most important, why this happened? Can anybody explain theses results?
> 
> Thanks for all
> Daniel
> 
> 
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